# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:10:26 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-[(2R)-2-carbamimidamido-2-cyclohexylacetyl]glycyl-N-(3-sulfanylpropyl)-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)CNC(=O)[C@H](NC(N)=N)C1CCCCC1)C(=O)NCCCS
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 NMP  NMP  N-[(2R)-2-carbamimidamido-2-cyclohexylacetyl]glycyl-N-(3-sulfanylpropyl)-L-alaninamide  ligand  59  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NMP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 NMP  S27   S  S2    0  -0.252  -1.4511   0.1623  -10.0176
 NMP  C26   C  CH2   0  -0.584  -0.5119  -0.7328   -8.7372
 NMP  C25   C  CH2   0  -0.487  -0.4418   0.1253   -7.4844
 NMP  C24   C  CH2   0  -0.206   0.3160  -0.5953   -6.3804
 NMP  N23   N  NH1   0  -0.676   0.3435   0.2151   -5.1793
 NMP  C20   C  C     0   0.595   1.0060  -0.1479   -4.0786
 NMP  O21   O  O     0  -0.458   1.6516  -1.1836   -3.9904
 NMP  C19   C  CH1   0  -0.198   0.9569   0.8578   -2.9326
 NMP  C22   C  CH3   0  -0.630   2.0534   1.9083   -3.1182
 NMP  N18   N  NH1   0  -0.675   1.1104   0.1269   -1.6974
 NMP  C16   C  C     0   0.541   0.6621   0.5709   -0.5181
 NMP  O17   O  O     0  -0.387   0.0559   1.6218   -0.3712
 NMP  C15   C  CH2   0  -0.401   0.9565  -0.3614    0.6451
 NMP  N14   N  NH1   0  -0.626   0.5110   0.2324    1.8724
 NMP  C6    C  C     0   0.599   0.6696  -0.3757    3.0593
 NMP  O7    O  O     0  -0.602   1.2205  -1.4592    3.1687
 NMP  C5    C  CH1   0  -0.186   0.1269   0.4040    4.2609
 NMP  N4    N  NH1   0  -0.660   1.1833   0.6524    5.2196
 NMP  C2    C  C     0   0.590   1.7359  -0.2588    6.0867
 NMP  N3    N  NH2   0  -0.845   2.9785   0.1476    6.5482
 NMP  N1    N  N     0  -0.664   1.1518  -1.3467    6.4150
 NMP  C8    C  CH1   0  -0.254  -1.1448  -0.2456    4.8197
 NMP  C9    C  CH2   0  -0.407  -1.6407   0.4880    6.0650
 NMP  C10   C  CH2   0  -0.411  -2.9414  -0.1107    6.5907
 NMP  C11   C  CH2   0  -0.438  -4.0248  -0.1303    5.5195
 NMP  C12   C  CH2   0  -0.429  -3.5390  -0.8612    4.2735
 NMP  C13   C  CH2   0  -0.413  -2.2382  -0.2644    3.7468
 NMP  H27   H  HSH1  0   0.226  -1.2666  -0.7082  -11.0154
 NMP  H261  H  HCH2  0   0.281   0.4898  -0.9461   -9.1101
 NMP  H262  H  HCH2  0   0.297  -1.0040  -1.6814   -8.5218
 NMP  H251  H  HCH2  0   0.225  -1.4534   0.3597   -7.1409
 NMP  H252  H  HCH2  0   0.301   0.0522   1.0731   -7.7128
 NMP  H241  H  HCH2  0   0.182   1.3373  -0.8054   -6.7057
 NMP  H242  H  HCH2  0   0.195  -0.1584  -1.5581   -6.1699
 NMP  H23   H  HNH1  0   0.395  -0.2268   1.0455   -5.1530
 NMP  H19   H  HCH1  0   0.288  -0.0150   1.3557   -2.9234
 NMP  H221  H  HCH3  0   0.192   3.0379   1.4409   -3.1410
 NMP  H222  H  HCH3  0   0.253   1.9141   2.4616   -4.0466
 NMP  H223  H  HCH3  0   0.269   2.0283   2.6212   -2.2957
 NMP  H18   H  HNH1  0   0.398   1.6387  -0.7330   -1.7393
 NMP  H151  H  HCH2  0   0.262   0.4605  -1.3202    0.4608
 NMP  H152  H  HCH2  0   0.307   2.0298  -0.5696    0.6782
 NMP  H14   H  HNH1  0   0.385   0.0450   1.1247    1.8102
 NMP  H5    H  HCH1  0   0.288  -0.1656   1.4014    3.9139
 NMP  H4    H  HNH1  0   0.393   1.8252   1.3591    4.8981
 NMP  H31   H  HNH2  0   0.377   3.2736  -0.3005    7.4010
 NMP  H32   H  HNH2  0   0.360   3.1434   1.1423    6.5863
 NMP  H1    H  H     0   0.310   1.7015  -1.8454    7.1054
 NMP  H8    H  HCH1  0   0.238  -0.9087  -1.2728    5.1034
 NMP  H91   H  HCH2  0   0.237  -0.8773   0.4516    6.8424
 NMP  H92   H  HCH2  0   0.170  -1.8011   1.5466    5.8248
 NMP  H101  H  HCH2  0   0.216  -2.7536  -1.1336    6.9359
 NMP  H102  H  HCH2  0   0.223  -3.2803   0.4508    7.4653
 NMP  H111  H  HCH2  0   0.216  -4.9360  -0.5967    5.9022
 NMP  H112  H  HCH2  0   0.206  -4.2899   0.8990    5.2533
 NMP  H121  H  HCH2  0   0.207  -3.3819  -1.9186    4.5121
 NMP  H122  H  HCH2  0   0.249  -4.3021  -0.8312    3.4920
 NMP  H131  H  HCH2  0   0.204  -2.4295   0.7597    3.4015
 NMP  H132  H  HCH2  0   0.213  -1.9139  -0.8295    2.8685

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 NMP  S27  C26   single  1.823  0.020  1.823
 NMP  S27  H27   single  1.200  0.020  1.300
 NMP  C26  C25   single  1.520  0.020  1.520
 NMP  C26  H261  single  0.970  0.020  1.090
 NMP  C26  H262  single  0.970  0.020  1.090
 NMP  C25  C24   single  1.521  0.020  1.521
 NMP  C25  H251  single  0.970  0.020  1.090
 NMP  C25  H252  single  0.970  0.020  1.090
 NMP  C24  N23   single  1.449  0.020  1.449
 NMP  C24  H241  single  0.970  0.020  1.090
 NMP  C24  H242  single  0.970  0.020  1.090
 NMP  N23  C20   single  1.335  0.020  1.335
 NMP  N23  H23   single  0.860  0.020  1.020
 NMP  C20  O21   double  1.224  0.020  1.224
 NMP  C20  C19   single  1.526  0.020  1.526
 NMP  C19  C22   single  1.530  0.020  1.530
 NMP  C19  N18   single  1.443  0.020  1.443
 NMP  C19  H19   single  0.970  0.020  1.090
 NMP  C22  H221  single  0.970  0.020  1.090
 NMP  C22  H222  single  0.970  0.020  1.090
 NMP  C22  H223  single  0.970  0.020  1.090
 NMP  N18  C16   single  1.337  0.020  1.337
 NMP  N18  H18   single  0.860  0.020  1.020
 NMP  C16  O17   double  1.222  0.020  1.222
 NMP  C16  C15   single  1.520  0.020  1.520
 NMP  C15  N14   single  1.434  0.020  1.434
 NMP  C15  H151  single  0.970  0.020  1.090
 NMP  C15  H152  single  0.970  0.020  1.090
 NMP  N14  C6    single  1.343  0.020  1.343
 NMP  N14  H14   single  0.860  0.020  1.020
 NMP  C6   O7    double  1.220  0.020  1.220
 NMP  C6   C5    single  1.532  0.020  1.532
 NMP  C5   N4    single  1.448  0.020  1.448
 NMP  C5   C8    single  1.533  0.020  1.533
 NMP  C5   H5    single  0.970  0.020  1.090
 NMP  N4   C2    single  1.374  0.020  1.374
 NMP  N4   H4    single  0.890  0.020  1.040
 NMP  C2   N3    single  1.386  0.020  1.386
 NMP  C2   N1    double  1.278  0.020  1.278
 NMP  N3   H31   single  0.890  0.020  1.040
 NMP  N3   H32   single  0.890  0.020  1.040
 NMP  N1   H1    single  0.890  0.020  1.040
 NMP  C8   C9    single  1.528  0.020  1.528
 NMP  C8   C13   single  1.532  0.020  1.532
 NMP  C8   H8    single  0.970  0.020  1.090
 NMP  C9   C10   single  1.525  0.020  1.525
 NMP  C9   H91   single  0.970  0.020  1.090
 NMP  C9   H92   single  0.970  0.020  1.090
 NMP  C10  C11   single  1.524  0.020  1.524
 NMP  C10  H101  single  0.970  0.020  1.090
 NMP  C10  H102  single  0.970  0.020  1.090
 NMP  C11  C12   single  1.524  0.020  1.524
 NMP  C11  H111  single  0.970  0.020  1.090
 NMP  C11  H112  single  0.970  0.020  1.090
 NMP  C12  C13   single  1.525  0.020  1.525
 NMP  C12  H121  single  0.970  0.020  1.090
 NMP  C12  H122  single  0.970  0.020  1.090
 NMP  C13  H131  single  0.970  0.020  1.090
 NMP  C13  H132  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 NMP  H27   S27  C26    97.66  3.000
 NMP  H262  C26  H261  108.19  3.000
 NMP  H262  C26  C25   110.44  3.000
 NMP  H261  C26  C25   110.49  3.000
 NMP  H262  C26  S27   109.48  3.000
 NMP  H261  C26  S27   109.23  3.000
 NMP  C25   C26  S27   108.99  3.000
 NMP  H252  C25  H251  107.32  3.000
 NMP  H252  C25  C24   109.72  3.000
 NMP  H251  C25  C24   109.54  3.000
 NMP  H252  C25  C26   109.76  3.000
 NMP  H251  C25  C26   109.70  3.000
 NMP  C24   C25  C26   110.72  3.000
 NMP  H242  C24  H241  107.08  3.000
 NMP  H242  C24  N23   109.94  3.000
 NMP  H241  C24  N23   109.68  3.000
 NMP  H242  C24  C25   109.92  3.000
 NMP  H241  C24  C25   109.93  3.000
 NMP  N23   C24  C25   110.25  3.000
 NMP  H23   N23  C20   118.91  3.000
 NMP  H23   N23  C24   118.15  3.000
 NMP  C20   N23  C24   122.73  3.000
 NMP  C19   C20  O21   121.39  3.000
 NMP  C19   C20  N23   115.10  3.000
 NMP  O21   C20  N23   123.46  3.000
 NMP  H19   C19  N18   108.56  3.000
 NMP  H19   C19  C22   109.01  3.000
 NMP  N18   C19  C22   112.05  3.000
 NMP  H19   C19  C20   109.61  3.000
 NMP  N18   C19  C20   107.80  3.000
 NMP  C22   C19  C20   109.78  3.000
 NMP  H223  C22  H222  107.95  3.000
 NMP  H223  C22  H221  108.50  3.000
 NMP  H222  C22  H221  108.38  3.000
 NMP  H223  C22  C19   109.97  3.000
 NMP  H222  C22  C19   111.13  3.000
 NMP  H221  C22  C19   110.82  3.000
 NMP  H18   N18  C16   119.64  3.000
 NMP  H18   N18  C19   116.82  3.000
 NMP  C16   N18  C19   123.42  3.000
 NMP  C15   C16  O17   122.12  3.000
 NMP  C15   C16  N18   113.98  3.000
 NMP  O17   C16  N18   123.90  3.000
 NMP  H152  C15  H151  106.43  3.000
 NMP  H152  C15  N14   110.96  3.000
 NMP  H151  C15  N14   111.46  3.000
 NMP  H152  C15  C16   109.27  3.000
 NMP  H151  C15  C16   108.70  3.000
 NMP  N14   C15  C16   109.92  3.000
 NMP  H14   N14  C6    120.64  3.000
 NMP  H14   N14  C15   117.19  3.000
 NMP  C6    N14  C15   122.14  3.000
 NMP  C5    C6   O7    122.79  3.000
 NMP  C5    C6   N14   114.90  3.000
 NMP  O7    C6   N14   122.31  3.000
 NMP  H5    C5   C8    106.24  3.000
 NMP  H5    C5   N4    104.37  3.000
 NMP  C8    C5   N4    115.88  3.000
 NMP  H5    C5   C6    108.02  3.000
 NMP  C8    C5   C6    111.35  3.000
 NMP  N4    C5   C6    110.38  3.000
 NMP  H4    N4   C2    114.24  3.000
 NMP  H4    N4   C5    111.95  3.000
 NMP  C2    N4   C5    126.69  3.000
 NMP  N1    C2   N3    125.02  3.000
 NMP  N1    C2   N4    122.89  3.000
 NMP  N3    C2   N4    112.09  3.000
 NMP  H32   N3   H31   111.02  3.000
 NMP  H32   N3   C2    116.62  3.000
 NMP  H31   N3   C2    114.45  3.000
 NMP  H1    N1   C2    110.24  3.000
 NMP  H8    C8   C13   108.96  3.000
 NMP  H8    C8   C9    108.07  3.000
 NMP  C13   C8   C9    110.18  3.000
 NMP  H8    C8   C5    108.30  3.000
 NMP  C13   C8   C5    109.99  3.000
 NMP  C9    C8   C5    111.26  3.000
 NMP  H92   C9   H91   106.90  3.000
 NMP  H92   C9   C10   109.23  3.000
 NMP  H91   C9   C10   109.77  3.000
 NMP  H92   C9   C8    109.41  3.000
 NMP  H91   C9   C8    109.75  3.000
 NMP  C10   C9   C8    111.66  3.000
 NMP  H102  C10  H101  106.30  3.000
 NMP  H102  C10  C11   110.40  3.000
 NMP  H101  C10  C11   109.35  3.000
 NMP  H102  C10  C9    109.78  3.000
 NMP  H101  C10  C9    109.20  3.000
 NMP  C11   C10  C9    111.66  3.000
 NMP  H112  C11  H111  106.52  3.000
 NMP  H112  C11  C12   109.21  3.000
 NMP  H111  C11  C12   110.33  3.000
 NMP  H112  C11  C10   109.31  3.000
 NMP  H111  C11  C10   110.61  3.000
 NMP  C12   C11  C10   110.75  3.000
 NMP  H122  C12  H121  106.41  3.000
 NMP  H122  C12  C13   109.75  3.000
 NMP  H121  C12  C13   109.30  3.000
 NMP  H122  C12  C11   110.42  3.000
 NMP  H121  C12  C11   109.31  3.000
 NMP  C13   C12  C11   111.51  3.000
 NMP  H132  C13  H131  106.33  3.000
 NMP  H132  C13  C12   109.16  3.000
 NMP  H131  C13  C12   108.97  3.000
 NMP  H132  C13  C8    110.93  3.000
 NMP  H131  C13  C8    109.47  3.000
 NMP  C12   C13  C8    111.82  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 NMP  CONST_01  O21  C20  N23  C24     0.00   0.0  0
 NMP  CONST_02  C19  C20  N23  C24   180.00   0.0  0
 NMP  CONST_03  O17  C16  N18  C19     0.00   0.0  0
 NMP  CONST_04  C15  C16  N18  C19   180.00   0.0  0
 NMP  CONST_05  O7   C6   N14  C15     0.00   0.0  0
 NMP  CONST_06  C5   C6   N14  C15   180.00   0.0  0
 NMP  CONST_09  H23  N23  C20  O21   180.00   0.0  0
 NMP  CONST_10  H18  N18  C16  O17   180.00   0.0  0
 NMP  CONST_11  H14  N14  C6   O7    180.00   0.0  0
 NMP  CONST_14  H1   N1   C2   N4    180.00   0.0  0
 NMP  CONST_15  H4   N4   C2   N3      0.00   0.0  0
 NMP  Var_01    C11  C10  C9   C8    -55.87  30.0  1
 NMP  Var_02    C11  C12  C13  C8     55.66  30.0  1
 NMP  Var_03    C12  C11  C10  C9     55.19  30.0  1
 NMP  Var_04    C13  C12  C11  C10   -55.04  30.0  1
 NMP  Var_05    C24  C25  C26  S27   179.08  30.0  3
 NMP  Var_06    N23  C24  C25  C26  -178.36  30.0  3
 NMP  Var_07    C20  N23  C24  C25  -176.32  30.0  3
 NMP  Var_08    N14  C15  C16  N18   176.60  30.0  3
 NMP  Var_09    C6   N14  C15  C16  -178.97  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NMP  chir_01  C19  C20  C22  N18  positiv
 NMP  chir_02  C5   N4   C6   C8   negativ
 NMP  chir_03  C8   C13  C9   C5   positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 NMP  plan-1  C24  0.020
 NMP  plan-1  N23  0.020
 NMP  plan-1  C20  0.020
 NMP  plan-1  O21  0.020
 NMP  plan-1  C19  0.020
 NMP  plan-1  H23  0.020
 NMP  plan-2  C19  0.020
 NMP  plan-2  N18  0.020
 NMP  plan-2  C16  0.020
 NMP  plan-2  O17  0.020
 NMP  plan-2  C15  0.020
 NMP  plan-2  H18  0.020
 NMP  plan-3  C15  0.020
 NMP  plan-3  N14  0.020
 NMP  plan-3  C6   0.020
 NMP  plan-3  O7   0.020
 NMP  plan-3  C5   0.020
 NMP  plan-3  H14  0.020
 NMP  plan-4  C5   0.020
 NMP  plan-4  N4   0.020
 NMP  plan-4  C2   0.020
 NMP  plan-4  N3   0.020
 NMP  plan-4  N1   0.020
 NMP  plan-4  H4   0.020
 NMP  plan-4  H31  0.020
 NMP  plan-4  H32  0.020
 NMP  plan-4  H1   0.020

